From textbook: Chapter 9 - Case Study - Predicting salmon populations - page 84

1. In the repository for this book, you’ll find a notebook called salmon.ipynb,
   which contains some data and code to get you started. Read through
   the notebook and run it.

There is no notebook named salmon.ipynb.
salmon_soln is found in the solution folder, but having to filter out exercise-text from the solution is not ideal

I got this book and I'm going through the exercises but I can't find the answers 🔑 anywhere. Am I missing something obvious? 😢

In chapter 2 of the textbook the show function is used to display the bikeshare state. Where is this function defined? I am trying (fairly successfully) to run the textbook in my local python environment instead of a workbook.

Hi;

I'm going through your book and I'm doing the Computation with units example.

When I run the following line:

t = math.sqrt(2 * h / a)

I get the following error:

I'm note sure how to trouble-shoot it.

Am I doing something wrong, or is there an issue with pint?

Thanks!

Solving for c...

https://allendowney.github.io/ModSimPy/chap14.html

When update_func() is set to return State with UNITS, run_simulation() crashes when tryin to enter the update_func() output into ModSimDataFrame().

A simple example : pressure increases with depth $dp = \rho dy g$, I initialize params with
( p = 0 * Pa, dy =0.1 * m , rho = 1000*kg/m**3) etc .....

I (think I) cannot use ode_solver since it is linked with time. So I constrct update_func() that retuns State(p=p,y=y), In run_simulation() I create frame=ModSimDataFrame(), use dimensionless

ts = linrange( 0,100,0.1)
for t in ts:

and when I try to

update frame[ t + dy ] = update_func(...)

it crashes. All is ok, wen I completely remove UNITS. Pitty, isnt it?

The queue case study has instructions to Set duration, which is the number of time steps to simulate, to 10 hours, expressed in minutes.

I did this in the following way

minutes = UNITS.minutes
hours = UNITS.hour
duration=(10*hours).to(minutes)

Later on, there is a prewritten function that uses the system duration to create a range

for t in linrange(0, system.duration):

When that runs, it gives me the following error:

---

DimensionalityError Traceback (most recent call last)
in ()
1 # Solution goes here
----> 2 results = run_simulation(system, update)
3 plot(results)

in run_simulation(system, update_func)
9 results[0] = x
10
---> 11 for t in linrange(0, system.duration):
12 x = update_func(x, t, system)
13 results[t+1] = x

~/projects/modsim.py in linrange(start, stop, step, **options)
178 n += 1
179
--> 180 array = np.linspace(start, stop, int(n), **options)
181 if units:
182 array = array * units

~/miniconda2/envs/simulation/lib/python3.7/site-packages/pint/quantity.py in int(self)
439 if self.dimensionless:
440 return int(self._convert_magnitude_not_inplace(UnitsContainer()))
--> 441 raise DimensionalityError(self._units, 'dimensionless')
442
443 def long(self):

DimensionalityError: Cannot convert from 'minute' to 'dimensionless'

Should duration not be using units, is there a way do create a range with units, or am I missing something simple?

https://allendowney.github.io/ModSimPy/chap17.html#data

data.head()

I had to grab some simple cart2pol code for something,when I came across this repo ,and saw this

I checked the codes and saw this is going to be tricky as the mag function above it already has the unit bound to it,else it would have just been np.arcos(np.dot(self,other)/self.mag* other.mag)
Just pointing it out.

Which we can write more concisely: $a=−rα$ This relationship

Hi, I have been trying to use your repository, however whenever I try to use from modsim import * it returns ModuleNotFoundError: No module named 'modsim' How would I go about fixing that?

Concerning the running simulations section, int() truncates and does not necessarily round down.
Kind of a minor nitpick, but feedback is feedback.

One of the exercises in the case study for the salmon population model (salmon.ipynb) mentions an object type called "ModeSimSeries". I am having trouble finding that type. It is not defined in modsim.py and according to the search function at allendowney.github.io/ModSimPy it is not mentioned in the text.

Am I missing something or is there something missing?

Hello,

I've just ordered the printed version of the book: Modeling and Simulation in Python

I would like to ask you if you know any starting example to simulate a simple production line in real time.
Or at least can you point me to a similar example?
I will need to change inputs in real time and use the outputs in a java application.

Thank you so much in advance.
Best,
Nelson

Hi,
Saw your lightning talk at SciPy, thought I would make a suggestion, as you had invited.

I had to reproduce a bacterial simulation for my bioinformatics class and I think it is a pretty doable example.

The paper is the following:
Counteraction of antibiotic production and degradation stabilizes microbial communities.
Kelsic ED, Zhao J, Vetsigian K, Kishony R.
Nature. 521(7553):516-9.
https://www.nature.com/nature/journal/v521/n7553/full/nature14485.html

The actual panel depicting a visualization of the simulation is Figure 1D.

I could supply the simulation in python, at the moment I only have a pretty version of it in R.

FutureWarning message:

/content/modsim.py:621: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for label, value in res.iteritems():

pd.Series.iteritems has been deprecated since pandas 1.5.0.

pd.Series.items is the recommended alternative: https://pandas.pydata.org/pandas-docs/version/1.5/reference/api/pandas.Series.items.html#pandas.Series.items

they should read
pip install ModSimPy
and not
pip install ModSim

In the "Parameters" section where you already have a "%TODO: expand this transition" you use the phrase "it would be better to generalize this function" so it takes the probabilities p1 and p2 as parameters:" and you haven't used this language before in the notebooks or textbook. In the relevant part of the textbook you do say, " The advantage of using parameters is that you can call the same function many times, providing different arguments each time." Perhaps you can explicitly describe this as generalization there and it will make more sense in the notebook.

I ran across the following error(s) when trying to run notebook code on binderhub.

Running the first cell in the chap02.ipynb notebook results in an error when modsim attempts to import solve_ivp from scipy. It appears that solve_ivp wasn't introduced until after scipy 0.19.1.

Unrelated, but the ast_node_interactivity value is also throwing an error (shown in screenshot below).

UnicodeDecodeError: 'gbk' codec can't decode byte 0x9d in position 4990: illegal multibyte sequence

I believe you meant one at a time.

Haven't dived too deeply into this, but I'm getting the feeling it isn't the intended behavior. There's a lot of weirdness that happens when multiplying a Pint Quantity by a modsim Vector(Quantity).

For example, this produces the expected result:

however accessing x or y produces an error:

distance_vector.x
# -> Neither Quantity object nor its magnitude ([ 0.5547002   0.83205029]) has attribute 'x'

here's a workaround:

acc = 1 * UNITS.m/UNITS.second**2 
acc = (acc.m * Vector(2,3).hat()) * acc.units
acc.x
# -> 0.5547001962252291 meter/second**2 :)

Unrelated, there's a weird edge case that brakes Pint's TeX formatting:

Looks like there's some kind of superscript formatting going on in the TeX source? Might be a bug on Pint's end.

The pint version (0.7.2) in the unidata channel is for Python 3.6. When installing it on the latest version of Anaconda with Python 3.7, this downgrades a large number of packages to Python 3.6. The conda-forge channel has the latest version of pint (0.9) for Python 3.7 and is referenced on the pint website. Unless the older version of pint is required, could you use the conda-forge channel instead?

Love the content, thanks for making it publicly available!

The "Click here to run this chapter on Colab" links in the notebooks are point to https://colab.research.google.com/github/AllenDowney/ModSimPy/blob/master//chapters/chap12.ipynb (for example in chapter 12 & 13, didn't check the others) - shouldn't they be linking to https://colab.research.google.com/github/AllenDowney/ModSimPy/blob/master/colab/chap12.ipynb instead?

Hey,

I'm trying to begin this book and when following the requirements it says to do pip install modsimpy. When I try to do so, it gives me a really long error message:

ERROR: Command errored out with exit status 1:
     command: 'C:\Users\Brady\Anaconda3\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\Brady\\AppData\\Local\\Temp\\pip-install-426xujgr\\modsimpy\\setup.py'"'"'; __file__='"'"'C:\\Users\\Brady\\AppData\\Local\\Temp\\pip-install-426xujgr\\modsimpy\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
         cwd: C:\Users\Brady\AppData\Local\Temp\pip-install-426xujgr\modsimpy\
    Complete output (9 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\Brady\AppData\Local\Temp\pip-install-426xujgr\modsimpy\setup.py", line 20, in <module>
        long_description=readme(),
      File "C:\Users\Brady\AppData\Local\Temp\pip-install-426xujgr\modsimpy\setup.py", line 6, in readme
        return f.read()
      File "C:\Users\Brady\Anaconda3\lib\encodings\cp1252.py", line 23, in decode
        return codecs.charmap_decode(input,self.errors,decoding_table)[0]
    UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 4990: character maps to <undefined>
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I have verified that I can install other packages with pip and I tried reinstalling pip using conda as well as restarting my computer.

How can I fix this? Or is there an alternate way of installing modsimpy now? Thanks!

this looks to be the first usage:

Looks like the definition should probably be here:

I am opening this issue to document my thinking about how to generate the LaTeX version of the book, and to solicit comments.

As of Version 4, the source of the books is the Jupyter notebooks. I use JupyterBook to generate the HTML version, which is hosted here on GitHub.

For publication, I would like to generate a LaTeX version.

I considered using nbconvert to convert from ipynb to tex, but the LaTeX that gets generated would be hard to work with.

A better option seems to be using nbconvert to generate Markdown and then use Pandoc to generate LaTeX.

Pandoc gets pretty close, with these command-line arguments:

--listings --top-level-division=chapter

But I will probably still have to do some post-processing:

1. The LaTeX files PanDoc generates are complete documents with frontmatter, etc. To convert these files to chapters that can be included in a top-level document, I'll have to strip some lines from the beginning and end.

2. Currently the images don't survive the translation process.

It seems like it will take some effort to get this working, so before I go too far down this path, I want to consider alternatives.

I welcome comments from anyone who reads this, but I'd like to ask @hamelsmu and @jph00 in particular to take a look. With your experience with fastdoc, you might have suggestions. Thanks!

In the Contributer List section of chapter 0, the second sentence reads "Or if your are a Git use, send me a pull request!"

In the Using a DataFrame section, a global variable sir is defined, but not used. The previously defined system variable is used in it's stead. Apart from confusion, this typo may confuse students when attempting to solve the subsequent exercise.

After following the installation instructions, I did import modsim and got the following errors (differentiated by Python 2.7 & 3.6). I'm running these on Anaconda 4.7.5

Python 3.6

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\hsamuel\AppData\Local\Continuum\anaconda2\envs\py36\lib\site-packages\modsim\__init__.py", line 1, in <module>
    from .modsim import *
  File "C:\Users\hsamuel\AppData\Local\Continuum\anaconda2\envs\py36\lib\site-packages\modsim\modsim.py", line 38, in <module>
    from pint.errors import UnitStrippedWarning
ImportError: cannot import name 'UnitStrippedWarning'

Python 2.7

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\hsamuel\AppData\Local\Continuum\anaconda2\lib\site-packages\modsim\__init__.py", line 1, in <module>
    from .modsim import *
  File "C:\Users\hsamuel\AppData\Local\Continuum\anaconda2\lib\site-packages\modsim\modsim.py", line 1668
    def Vector(*args, units=None):
                          ^
SyntaxError: invalid syntax

In chapter 01, In [57]:

assert abs(v.magnitude - 86.41527642726142) < 1e7

Shouldn't this be:

assert abs(v.magnitude - 86.41527642726142) < 1e-7

I was able to upload the Jupyter notebooks for chapters 1-4 of ModSimPy but attempting Chapter 5 (chap05.ipynb) led to the following error:

error was: SyntaxError: JSON Parse error: Unrecognized token '<'

Downloaded current version (as of April 2021) Anaconda Python 3.8
UnsatisfiableError when trying conda install -c unidata pint as in book Release 4:

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

• pint -> python[version='2.7.|3.4.|3.5.|3.6.']

Your python: python=3.8

Thanks for looking into it.

Viewing modsim/test_modsim.py in VSC with PyLance shows a lot of errors.

A lot of functions are missing.

An object can't be an instance of a function.

pint is not used, and also UnitStrippedWarning

Hola Profesor Allen,

In this line it should be
for p2 in p2_array:
instead of
for p2 in p1_array:

Have a good day.

plot(results, label='Olin')

should be

plt.plot(results, label='Olin')

Hi,
Could anyone help me?
I am try to execute examples from chapter 18. I am facing this issue with multiple assignment G, X = state
in slope_func. where G and X assigned randomly to values inside state but not on position basis. which is creating further problem.
I tried to assign G = state.G and X = state.X but that cause problem while running run_ode_solver and shows AttributeError: 'numpy.ndarray' object has no attribute 'G'

Hi Allen,

Something is wrong with the "results" after change the range in a for loop from a number to a minor number, for example I run this:

In [47]:
for i in range(10):
step(0.3, 0.2)
results[i] = bikeshare.olin

Displays:

values

0 | 5
1 | 5
2 | 4
3 | 4
4 | 5
5 | 5
6 | 5
7 | 4
8 | 3
9 | 2

But when I changed to this:

In [47]:
for i in range(6):
step(0.3, 0.2)
results[i] = bikeshare.olin

Displays:

values

0 | 2
1 | 1
2 | 1
3 | 0
4 | -1
5 | -1
6 | 5
7 | 4
8 | 3
9 | 2

I dont understand why the values are indexed to 10 positions after run the code with a range of 6 positions.

Thanks in advanced!

The following code results in a Pandas KeyError:

import modsim
foo = modsim.modsim.ModSimSeries([])
dir(foo)  # KeyError: 'dt'

This seems to be the result of the definition of ModSimSeries, in which the property definitions of dt and T call pandas.Series.loc. As a result, when calling dir(foo), the standard Python library (accessor.py) seems to try to get a nonexistent row.

Oddly, defining only dt as a row index in the series seems to fix this:

import modsim
bar = modsim.modsim.ModSimSeries({'dt': 2})
dir(bar)  # Works as expected

I suspect that this can be handled by overriding the default __getattribute__ or __getattr__ in ModSimSeries.

I want to know where I can find the answers to the exercises in each chapter.
Thank you！

The documentation for modsim.py's fsolve says that x0 can be a scalar or array, matching scipy's api (well, its defecto one – in the docs it only mentions arrays) . However the sanity check passing x0 into func at the modsim level assumes a scalar type, making arrays not usable.

Expected behavior

def func(x):
    return (x-1) * (x-2) * (x-3)

fsolve(func, x0=[0,5])
# -> array([ 1.,  3.])

scipy.optimize.fsolve(func, x0=(0,5))
# -> array([ 1.,  3.])

Actual behavior

def func(x):
    return (x-1) * (x-2) * (x-3)

fsolve(func, x0=[0,5])
# -> TypeError: unsupported operand type(s) for -: 'list' and 'int'

scipy.optimize.fsolve(func, x0=(0,5))
# -> array([ 1.,  3.])